The High Level Inter-Ministerial Committee (CIMIN) is at the top level of EMF organization. The body is composed by Chiefs of Defence (CHOD), Political Head Directorates of Defence and Foreign Affairs Ministries and credited representatives of participating nations. The CIMIN ensures the politico-military direction of the participating countries establishes the conditions for the employment of the force and issues directives to COMEUROMARFOR. CIMIN meetings are convoked when necessary, at the request of any of the member states.

The Politico-Military Working Group (POLMIL WG) is the executive body of CIMIN. The POLMIL WG is composed by the representatives from the CHOD's and from the Ministry of Foreign Affairs of the member countries. It takes care of all the activities related to the development and external relations of the Force and ensures the implementation of the CIMIN decisions. The POLMIL WG also appoints a Staff of the EMF countries to act as CIMIN Secretariat, for the conduct of its daily activities and to act as the permanent interlocutor of the CEMF.

Under the POLMIL WG, is the EUROMARFOR Sub working group (EMF SWG). EMF SWG is composed by representatives from each one of the Nation's Naval General Staffs mainly to advice the POLMIL WG on specific Naval issues and to express the single National Naval Staff's view on specific issues of own competence and co-ordinate positions and actions to be taken.

At the operational level of the chain of command, there is the Commander of the European Maritime Force (CEMF) or COMEUROMARFOR, who is designated every two years among the National Naval Authorities (NNAs) entities namely:

The CEMF relies both on his own existing National Staff and the EMF Permanent Cell (EMFPC) for the accomplishment of the assigned duties. The EMF is composed by Director who is an Officer of the same nationality as the CEMF and four representatives (Commanders or Lieutenant Commanders), one from each EMF Nation. Additionally, since November 2001 one Officer from Greece and one from Turkey joined the permanent cell as observers.